netZooR
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see netZooR.
Unified methods for the inference and analysis of gene regulatory networks
Bioconductor version: 3.16
netZooR unifies the implementations of several Network Zoo methods (netzoo, netzoo.github.io) into a single package by creating interfaces between network inference and network analysis methods. Currently, the package has 3 methods for network inference including PANDA and its optimized implementation OTTER (network reconstruction using mutliple lines of biological evidence), LIONESS (single-sample network inference), and EGRET (genotype-specific networks). Network analysis methods include CONDOR (community detection), ALPACA (differential community detection), CRANE (significance estimation of differential modules), MONSTER (estimation of network transition states). In addition, YARN allows to process gene expresssion data for tissue-specific analyses and SAMBAR infers missing mutation data based on pathway information.
Author: Marouen Ben Guebila [aut, cre] 
, Tian Wang [aut] , John Platig [aut], Marieke Kuijjer [aut] , Megha Padi [aut] , Rebekka Burkholz [aut], Des Weighill [aut] , Kate Shutta [ctb]
Maintainer: Marouen Ben Guebila <benguebila at hsph.harvard.edu>
citation("netZooR")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("netZooR")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("netZooR")| CONDOR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, GeneRegulation, GraphAndNetwork, Microarray, Network, NetworkInference, Software, Transcription |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2 years) |
| License | GPL-3 |
| Depends | R (>= 4.2.0), igraph, reticulate, pandaR, yarn |
| Imports | RCy3, viridisLite, STRINGdb, Biobase, GOstats, AnnotationDbi, matrixStats, GO.db, org.Hs.eg.db, Matrix, gplots, nnet, data.table, vegan, stats, utils, reshape, reshape2, penalized, parallel, doParallel, foreach, ggplot2, ggdendro, grid, MASS, assertthat, tidyr, methods, dplyr, graphics |
| System Requirements | |
| URL | https://github.com/netZoo/netZooR https://netzoo.github.io/ |
| Bug Reports | https://github.com/netZoo/netZooR/issues |
See More
| Suggests | testthat (>= 2.1.0), knitr, rmarkdown, pkgdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | netZooR_1.2.0.tar.gz |
| Windows Binary | netZooR_1.2.0.zip |
| macOS Binary (x86_64) | netZooR_1.2.0.tgz |
| macOS Binary (arm64) | netZooR_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/netZooR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/netZooR |
| Bioc Package Browser | https://code.bioconductor.org/browse/netZooR/ |
| Package Short Url | https://bioconductor.org/packages/netZooR/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.16 | Source Archive |